LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
  using 1 OpenMP thread(s) per MPI task
# Initialization
units           metal
boundary        p p p
atom_style      full
processors      * * 1     # domain decomposition over x and y

# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately

read_data       Bi_gr_AB_stack_2L_noH.data
  orthogonal box = (0 0 0) to (42.6 41.8117 100)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  1360 atoms
  0 = max # of 1-2 neighbors
  0 = max # of 1-3 neighbors
  0 = max # of 1-4 neighbors
  1 = max # of special neighbors
  special bonds CPU = 0.000143357 secs
  read_data CPU = 0.00128686 secs
mass            1 12.0107   # carbon mass (g/mole) | membrane
mass            2 12.0107   # carbon mass (g/mole) | adsorbate
# Separate atom groups
group		layer1 molecule 1
680 atoms in group layer1
group		layer2 molecule 2
680 atoms in group layer2

######################## Potential defition ########################
pair_style  hybrid/overlay  rebo  kolmogorov/crespi/full 16.0 1
####################################################################
pair_coeff  * * rebo               	 CH.rebo      C  C  # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff  * * kolmogorov/crespi/full   CH_taper.KC  C  C  # long range
####################################################################
# Neighbor update settings
neighbor        2.0 bin
neigh_modify    every 1
neigh_modify    delay 0
neigh_modify    check yes

#### Simulation settings ####
timestep	0.001
velocity	all create 300.0 12345

compute   	0 all pair rebo
compute  	1 all pair kolmogorov/crespi/full
variable  	REBO  equal c_0     # REBO energy
variable  	KC    equal c_1     # total interlayer energy
variable  	Evdw  equal c_1[1]  # attractive energy
variable 	Erep  equal c_1[2]  # repulsive  energy

############################

# Output
thermo          100
thermo_style    custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
thermo_modify   line one format float %.16f
thermo_modify   flush yes norm no lost warn

###### Run molecular dynamics ######
fix       	thermostat all nve
run 	  	1000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 18
  ghost atom cutoff = 18
  binsize = 9, bins = 5 5 12
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair rebo, perpetual
      attributes: full, newton on, ghost
      pair build: full/bin/ghost
      stencil: full/ghost/bin/3d
      bin: standard
  (2) pair kolmogorov/crespi/full, perpetual, copy from (1)
      attributes: full, newton on, ghost
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 17.21 | 17.21 | 17.21 Mbytes
Step CPU TotEng PotEng KinEng v_REBO v_KC v_Erep v_Evdw Temp 
       0 0.0000000000000000 -10037.7640583248121402 -10090.4634194413119985 52.6993611164999436 -10057.1894932863488066 -33.2739261549639664 35.9559834316876348 -69.2299095866357561 299.9999999999996589 
     100 5.3877589240437374 -10037.5122858156355505 -10065.4637593850693520 27.9514735694345475 -10032.2132655062632693 -33.2504938788055995 25.2100699045900747 -58.4605637833913789 159.1184768311149185 
     200 10.7755050340201706 -10037.4414086674350983 -10061.6271012692632212 24.1856926018286202 -10028.9093252939674130 -32.7177759752951403 18.5366534598604176 -51.2544294351563394 137.6811336385792970 
     300 16.1665089030284435 -10037.4824653300311184 -10064.2845326005663082 26.8020672705344225 -10030.9195389405322203 -33.3649936600345924 26.3639208740001152 -59.7289145340284122 152.5752876469470891 
     400 21.5454839280573651 -10037.5105626329259394 -10064.8769084956420556 27.3663458627154164 -10031.8478821022799821 -33.0290263933626349 36.6142885774199272 -69.6433149707719963 155.7875386888538571 
     500 26.9370588400634006 -10037.5010433785082569 -10064.8363209936451312 27.3352776151367571 -10031.4417172103931080 -33.3946037832518243 26.2980262321670750 -59.6926300154142595 155.6106774503846850 
     600 32.4204196080099791 -10037.4817772372425679 -10064.1925798287738871 26.7108025915316247 -10031.4376178099264507 -32.7549620188478201 18.5745873777024606 -51.3295493965519327 152.0557480714992380 
     700 37.8001567909959704 -10037.4834430268438155 -10064.1291975032218033 26.6457544763788299 -10030.8722888097800023 -33.2569086934421492 25.2322818106646771 -58.4891905041015008 151.6854507067418467 
     800 43.1622281169984490 -10037.5047888097760733 -10064.8671187128948077 27.3623299031188978 -10031.9815058608437539 -32.8856128520517217 36.5236695083771536 -69.4092823604148350 155.7646771616279011 
     900 48.5261204120470211 -10037.5068323940176924 -10065.3998155271074211 27.8929831330889542 -10032.1734374829957233 -33.2263780441125931 27.7314849391008309 -60.9578629832065317 158.7855101588076820 
    1000 53.8888844919856638 -10037.4811494880468672 -10064.0099109142265661 26.5287614261789670 -10031.3325267421259923 -32.6773841721003464 18.9005970229871600 -51.5779811950879434 151.0194480396057202 
Loop time of 53.8889 on 1 procs for 1000 steps with 1360 atoms

Performance: 1.603 ns/day, 14.969 hours/ns, 18.557 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 53.836     | 53.836     | 53.836     |   0.0 | 99.90
Bond    | 0.00043479 | 0.00043479 | 0.00043479 |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.032452   | 0.032452   | 0.032452   |   0.0 |  0.06
Output  | 0.00058326 | 0.00058326 | 0.00058326 |   0.0 |  0.00
Modify  | 0.0094135  | 0.0094135  | 0.0094135  |   0.0 |  0.02
Other   |            | 0.009815   |            |       |  0.02

Nlocal:    1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    7964 ave 7964 max 7964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  1.037e+06 ave 1.037e+06 max 1.037e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1037000
Ave neighs/atom = 762.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:54
